Metal Gear Solid: Philanthropy
by MrStagg
Summary: Nevada, 2006. A lone man camouflages himself among some rocks, overlooking a large military installation and Corporate outpost of ArmsTech/DARPA. Set between the events of Metal Gear Solid 1 and 2, the story follows the actions of Philanthropy as Snake and Otacon hunt intelligence related to a new Metal Gear.
1. Prologue: Shadows and Dust

**DISCLAIMER**

**I have just joined the world of FanFiction, and this is my first real attempt at a story. Any feedback on my work so far, whether the introduction is gripping etc, or any criticisms given are welcome. Hopefully this will turn into a full-fledged story at a later date. I will get to work on Chapter 2!**

**Thanks,**

**MrStagg**

Nevada, USA.

2006

0130

The cold, dusty landscape of the desert lay tranquil in the partial moonlight. A light wind rolled across the ground for miles around, adding a bit of bite to the cold night air. But disturbing the natural, rolling hills and desert was a collection of buildings. A military base and corporate HQ. The compound was over 3 square miles in size, and ringed by enough perimeter fence to stop an army. Floodlights mounted on huge stands illuminated the collection of buildings, courtyards and the landing pad located within the bounds of the fence. Towers dotted the perimeter, spotlights manned by security staff sweeping across the concrete and gravel every minute or so.

_Ordinary security guards? Unlikely._

Across from the base, a shadowy shape was barely visible on the hills to the South.

Slowly moving, so as to avoid detection despite the fact he was almost invisible, the man crawled towards a small cluster of rocks, the dusty, hard ground scratching uncomfortably beneath his body. When he was in cover, he stopped, reaching into a pouch to take out a set of binoculars. Bringing them up to his grey-blue eyes, he began to survey the scene.

The base was clearly visible against the oppressive darkness of the moonlit desert around it, but even so a good minute of surveillance could mean the difference between a successful infiltration and a failure. Sweeping the binoculars slowly around the base, the man noticed that there appeared to be a small section of perimeter fence which was indented slightly, as if some animal or rock had hit it – spying a possible opening, he looked to see what the fence opened out into: a vehicle yard, with trucks and jeeps parked in neat rows all the way along.

_Perfect._

Moving into a crouch, the moonlight caught his face for a moment. He had a grizzled, coarse-looking face with prominent cheeks and a small beard. His brown swept-back hair was held in place by a dark blue bandana, one of his prized possessions.

The man was Solid Snake.

He was a legend who, one year previous, had fought his arch-nemesis and twin, Liquid Snake, to the death after destroying the weapon of mass destruction Metal Gear REX, capable of launching unrestricted, un-trackable nuclear warheads from wherever the bipedal monstrosity was deployed. Following his escape from the icy Fox Archipelago in Alaska, specifically Shadow Moses Island (the base where REX was being built), Snake and Hal "Otacon" Emmerich formed the anti-Metal Gear group "Philanthropy", a fringe organisation targeting new Metal Gear weapons, after the schematics and data from REX was leaked onto the black market.

After being betrayed by the Secretary of Defence and left for dead at Shadow Moses, Snake and Otacon were labelled as terrorists and criminals, hunted by the CIA for crimes they did not commit. In the meantime, they lived on the run, across the entirety of the USA, Otacon's computer skills providing them with the time they needed to relocate when forces were closing on their position.

All that time, over a year since Shadow Moses, they were searching continually for intelligence related to new Metal Gears, and to destroy prototypes, weapon systems and computer software if necessary. Metal Gear, the ultimate weapon of mass destruction, could not be permitted to exist.

The reason a man like Snake was out here, in the middle of the desert in the cold and the dark, was because he and Otacon were onto something. Something big.

Somewhere inside that base, among the deepest, most secure systems in its computer mainframe was intelligence relating to a new Metal Gear design, one that Snake and Otacon had been on the trail of for over two months now.

Snake heard a CODEC call coming in, so he pressed his fingers to his right ear, opening up a sub-vocal communication channel using encrypted short-burst transmissions.

_"Snake? Are you receiving me?" _Otacon's voice crackled slightly into Snake's ear.

"Yeah, I can hear you Otacon, though it looks like there's a bit of interference" Snake replied in his gravelly tone.

_"Don't worry about it Snake – it's most likely the dust in the air, the wind is beginning to pick up a bit. As a matter of fact, we have storm warnings, so there may well be a dust storm later on this morning, after the sun is up. Now, let's recap on the objectives..."_


	2. Briefing: Breadcrumbs and Data Trails

**DISCLAIMER**

**Here's Chapter 2, which is sort of the final part of the introduction. Things get moving in Chapter 3, which I am now working on!**

**MrStagg**

Three weeks earlier...

Boston, MA

Current Philanthropy HQ

1130

The sweat glistened off of Snake's scarred body as he battered the punch bag, his thought focused on his exercise routine. When he wasn't training his CQC, Snake took to training other forms of unarmed combat, should the need arise to combine them to take apart enemies skilled in particular fields. Jabs and hooks flew at breakneck speed into the bag, which was shaking with force of the impacts, fist marks clearly visible along the surface of it.

Snake didn't seem to notice that his hands, which were not gloved, were bleeding somewhat around the knuckles. If anything, his mind seemed to be drifting from the combat training going before him and looking somewhere else entirely...

...The cold of the large hangar was counteracted by the warmth from the fires that had sprung up all over REX's armour. Snake's stinger missiles combined with the heroic efforts of Frank Jaeger, also known infamously as Gray Fox, had reduced REX's functionality to zero. However Liquid Snake, with his brutality, hatred and strength, remained unbeaten...

The force of a particularly powerful impact shook Snake's arm slightly.

...Snake was circling Liquid atop REX's head. Both men were covered in a sheen of sweat, cuts, bruises and lacerations, their condition only exacerbated by the painful intensity of the heat now coming from the smoke and roaring blazes all over REX's crippled form. Liquid's face was contorted into a snarl of total hatred, his soot-darkened blonde hair flowing behind him as he swung his right fist with all his might, Snake ducking under it and placing a few jabs of such power as would crush an ordinary man's ribs into Liquid's exposed chest. Roaring in pain, Liquid turned, the agony of the beatings both men were receiving only seeming to strengthen his anger. But Snake was more cool-headed at this point, closer to a point of relaxed and in total control, however his anger at Liquid for having killed so many people was stopping him reaching it. The worst pain of all was for Gray Fox, one of Snake's oldest friends and later enemies, who helped fight REX with him, as well as his fear for Meryl Silverburgh's life, her having sustained severe gunshot wounds at the hands of Sniper Wolf, whom Snake had fought and killed a few hours previously...

Snake was panting with exertion, but only seemed to be attacking the bag with renewed ferocity. Some of the seams were beginning to strain with the impacts, yet Snake continued relentlessly.

...Liquid was tilting, on the edge of Rex's head. Time seemed to slow down, as his arms waved in that way they do when a person is about to slip and fall, his expression of horror clearly visible, his pale eyes boring into Snake's skull, the hatred between them not forgotten as he slipped backwards into the darkness...

The bag was visibly tearing slightly at this point, small trickles of sand creating miniature dunes on the concrete floor. Snake was grunting with each impact, yet his arms only swung harder, blood flowing freely from his hands and dripping onto the growing piles of sand, turning it a muddy red.

...Snake and Meryl were struggling under the weight of their burned-out jeep, the shocking cold of the ice and snow causing agony on Snake's skin. The freezing air whipped past them, with a drop behind them over the cliff of well over fifty feet, and the remains of Liquid's own jeep burning a short way away. Snake wanted to get out from under the bulk of their jeep, to save Meryl, to get away from Shadow Moses and put a hundred miles between him and it. Struggling to move, but making small headway, Snake stopped suddenly as he saw a blurry, rippling figure struggle to stand behind the heat wash from the fires. A man with blonde hair, and an assault rifle in his right hand...

Ripping noises were spreading as the bag began to buckle under Snake's assault. His fists moving at almost superhuman speed, Snake pummelled the bag as if it were a living enemy, the flesh on his hands torn and bleeding steadily.

...Liquid was collapsing, his muscles clenching in pain as he suffered the massive cell death in the form of apoptosis in the heart inducing a fatal heart attack, caused by FOXDIE, the disease in Snake's blood. It was injected by Dr. Naomi Hunter, a woman who betrayed Snake for revenge against him, for crippling Frank Jaeger and initiating his transformation by surgery into Gray Fox, back in Zanzibarland.

Liquid cried out as he died.

"SNAKE!"

...Snake yelled out, a guttural roar of fury as his fist tore all the way through the leathery surface of the bag, the lower half dropping onto the floor with a bang as sand exploded outwards in all directions. The sweat dripped from Snake's brow, and his eyes were slightly unfocused as his attention returned to the drab concrete room in which he practised. Sensing the damage he had caused and his focus now back in reality; Snake mentally kicked himself for a moment for letting his memories of that place surface and get to him again.

_He's dead, Snake. He died and will remain dead. Shadow Moses is dead. The FOXHOUND unit are dead. Gray Fox is dead. They are dead and you survive. Let them go._

His rage left him, leaving in place a void, filled now by the intense pain in his hands, which were now bleeding so severely it was trickling down his forearm as he raised them to examine the damage. He thought of the serenity he experienced while retired in Alaska, with nothing to worry about but firewood and his huskies. He could feel the cold on his skin, revitalising him, calming him, clearing his mind and purging his body of emotion.

"Snake?" Otcaon's voice broke Snake's quiet zone. There was an element of worry in his tone; no doubt from the racket Snake was making destroying the punch bag. Snake took a deep breath.

_In for 10 seconds, out for 15. Lose the air and tension, squeeze the trigger..._

Snake shook his head slightly to clear those thoughts from his head. He was a trained killer, he always would be. Just a soldier, not a legend; but a soldier and killer all the same.

Letting the tension go from his muscles Snake calmed his heart rate and began to relax.

"I'm fine Otacon, just practising." Snake smiled a little when the look on Otacon's face when he saw the mess he had made flashed into his head. However, something would have to be done about his hands.

"Alright Snake, come down when you're ready, I think I have something on that new Metal Gear", Otacon's voice called from down the metal stairs into an even lower section of their basement of an HQ.

That shook Snake out of his reminiscing entirely. They had been on the trail of a new Metal Gear model for over a month after Otacon had intercepted messages and whispers over the incredible expanse of military and corporate networks all over the world, and this one, instead of recent attempts by rebel countries in Africa to build technology far beyond their capabilities, was centred around ArmsTech and DARPA, the two organisations responsible for building REX, and as such was somewhere in the US. Snake could feel his thoughts begin to race, the anticipation making his bloody palms sweat slightly.

_If we find this thing, we can take it down. ArmsTech and DARPA are a lethal combination of resources and data. This design is going to trump every one we have encountered so far, I know it._

Snake went through a low door into a small and rather dirty bathroom, illuminated by a solitary bulb on the ceiling.

_Can't pick and choose when you're a fugitive right? Ha ha._

Chuckling quietly to himself, Snake approached the medicine cabinet, where all the medical supplies would be stored. Opening it he took a liberal roll of bandages and some antiseptic. The pain in his hands had settled to a steady, painful throbbing, and the bleeding had slowed considerably, so Snake concluded that his knuckles were not split and no overly serious damage had been caused.

_This is going to sting._

He splashed doses of the water-based antiseptic onto the bandages and began to wrap them. Immediately the throbbing turned into agonising, searing pain. Snake had to clench his teeth to not cry out, and even then gasped slightly with the pain, but continued to wrap up his hands. Shortly after, they were neatly wrapped in bandages and the pain had almost fully subsided. Looking at his reflection in the grubby mirror, Snake saw the resemblance between himself, Liquid and his biological original Big Boss, the Legendary Soldier. Gaunt cheeks, a strong jaw, prominent facial hair and abilities in combat that matched each other, particularly in physical prowess and intelligence, to name a few traits. Both were dead now though, and Snake was the last one left.

Deciding that he had spent enough time gazing at his own reflection and the shadows that it mimicked, he walked out of the room, past the ruined punch bag, and down the metal stairs to their "Operations Room".

In actuality, the Operations Room consisted of a few chairs, a table, projector and Otcaon's massive computer workstation.

As if he had never left his quiet office on Shadow Moses, Otacon had a large desk with several computer screens mounted on it, as well as servers and computer towers whirring away beneath it. A sea of cables and wires ran across the floor into multiple plug sockets, making Snake wonder for a moment how Otacon managed to get enough power to this dingy basement in Boston without drawing attention from people who could give them away or hunt them down themselves.

"Hey Snake, I'll be with you in a minute." Otacon said over his shoulder as he tapped away at his keyboard, program windows flashing up on the screen for mere seconds while Otacon hunted for data in the lines of code. One of Otacon's qualities that truly surprised Snake was is expertise with computers. He could break into almost any system worldwide and steal any information he wanted.

_ In a different life, he would make a superb bank robber._

Snake sat down on one of the chairs quietly and waited for Otacon to finish. Acknowledging the usual health risks, and disregarding them completely, Snake took out a packet of his favourite cigarettes, and lit one with his lighter. He didn't need to worry about fumes, as this dingy basement had a few tricks, such as a high-standard air filtration and circulation system that was much harder to detect than normal above-ground vents. Lighting up his cigarette, the glow emitted by the burst of light from the lighter illuminating his face considerably against the dimmed brightness from the artificial lights, he inhaled deeply, then let out the smoke in a slow stream, almost sighing with relaxation as he did so, and enjoying the feeling of calm attentiveness the miniature rush from the cigarettes gave him.

"Okay, Snake. Here's what I have been able to dig up so far," Otacon said loudly enough to get Snake's attention. "A few weeks ago as you know, we caught wind of a new, far more advanced Metal Gear Project being commissioned. We don't know any timeframes, method or schematics, but we do know that it is being backed by ArmsTech/DARPA as a joint project. That alone is worrying enough, considering they built REX." Otacon shuddered slightly at the memory, no doubt form the crushing guilt he felt the and still felt now about his involvement in building the most devastating weapon mankind had ever seen.

"They have the resources to back it Otacon, and that much even I can work out," Snake replied gruffly. "But we don't know anything else about it, do we?"

"Almost, Snake." Otacon replied slowly, the anticipation in his voice matching a small, determined twinkle in his eye. "While we know no more about this new project, we do now know where we are going to find out about it."

Snake sat up slightly, the hairs on the back of his neck prickling, as they always did when he felt a surge of curiosity and interestingly this time, a hint of fear. They had faced down a few groups planning on building a new Metal Gear already, but not another Metal Gear itself, and if they knew so little about it, with such well-funded groups were backing its construction, then they were looking at fighting a fully prepared and active Metal Gear, ready to unleash Armageddon.

"I have been following a trail of digital breadcrumbs Snake," said Otacon with a hint of pride, notably in his ability to follow a trail of encoded, scrambled and disguised data to a new clue in his cyber-sleuthing. "I followed tiny packets of data and information to this." Bringing it up on the projector, a clear set of coordinates flashed up onto the wall.

"These coordinates correspond to a location in the Nevada desert, Snake. _A military installation_. Off the grid, not available on any conventional satellite viewing system, and not listed under any official property ownership in the entire state. But I tracked it down, and hacked my way into a military satellite, and I found this."

Changing up from the digits a black-and-white aerial image was shown – a compound, ringed in fences, with what looked like towers, courtyards and vehicle parks across the base, with a main collection of around 4 large buildings in the centre was blown up to a large size on the wall."

"This facility, Snake, doesn't exist officially. Unofficially, it is a corporate outpost of ArmsTech, with DARPA technicians making regular *ahem* 'business trips'. We may or may not have found the Metal Gear, Snake, but we have at least found the way to find it. Somewhere in their computer mainframe will be a folder, file or piece of data, _something_ that will lead us to their project."

"And let me guess, I need to sneak in and find the computer, then plug you in remotely and let you do the work?" Snake interrupted, attempting to predict how this was going to turn out.

"Actually Snake, their network is secure. No wireless connectivity I'm afraid. Which means you have got to do this one all by yourself" said Otacon while Snake groaned with despair "but hey, don't worry! I'll be with you every step of the way via CODEC. I can instruct you on where to look." A hint of cheerfulness had entered Otacon's voice.

"When do we get moving?" asked Snake quietly.

"Two days."


	3. Chapter 1: Doubts

_"So remember our aim here Snake. Get into the base, find and break into the mainframe, then we see about getting that data." _Otacon's voice crackled over the CODEC.

"Alright, but Otacon, there is a larger security detail here than the skeleton staff I was expecting," Snake muttered. "This mission is going to be a lot harder when we have so many guards to account for."

_"Don't worry about that Snake. I took precautions against such an unexpected turn of events – we have contact with someone on the inside Snake. A man I met while I was working on REX. His name is Corporal Robert Flynn, a minor member of the security team that I did a few favours for at Moses. When I made contact with him I told him that you would need to find him on site. He agreed to wear a red cloth around his neck, over his uniform so you could see it."_

"Thanks Otacon. What kind of help will he be able to provide?" Snake was pleasantly surprised at the lengths his friend went to to ensure the mission was a success.

_We must really need that data, _Snake thought.

_"He can give you schematics for the sub basements and the underground parts of the base overall, as well as minor access codes and advice on patrol patterns."_

"He won't be raising his weapon to help me then?" Snake asked, already sure of the answer.

_"Unfortunately, no. This is still a solo sneaking mission Snake, although he might be able to provide the location of the armoury for the staff, maybe you could procure some more firepower there if you need to?"_ Otacon suggested.

"Sounds like a good plan Otacon. When is my extraction?"

_"I'll be coming to pick you up in the chopper at 0530, two clicks from here, if everything goes to plan."_

"Four hours? Check. Alright Otacon, I'm moving in now."

_"Contact me if you need me Snake. My frequency is 141.12."_

Taking his hand off of his ear, Snake checked the pouches on his sneaking suit. A new innovation from Otacon, this suit fit Snake's body like a glove, was water and weatherproof, capable of many extra parts being worn (such as the combat vest Snake was wearing at the moment) as well as being difficult to spot in darkness. The perfect aid to Snake's infiltration.

His short pouch check complete, Snake pulled out a pistol from his thigh-holster. It was a Colt M1911 pistol, modified in the extreme by Otacon and himself, with a larger magazine, lower muzzle velocity for quiet functionality and a silencer supplied with it. Checking the slide, making sure there was a round in the chamber and that he had a full clip loaded, Snake clicked the weapon ready, and then switched the thumb safety on. He wasn't planning on racking up a body count tonight.

The disturbed section of the fence he spotted earlier was on the Western side of the compound, Snake currently being past the South fence. Snake, steeling his will for the coming task, set off across the low hills surrounding the base to reach the entry point. Moving in a low crouch, and stopping whenever he thought he was in eyesight, after a little while Snake was now looking down across the unlit open ground between his position and the dented part of the fence. Since he had packed bolt-cutters in order to enter the base, he was prepared enough to break the fencing. Moving now in a crawl, Snake took his time, making each small shuffle carefully and slowly. Snake was watching the closest guard tower, which was on his right, to see any signs whatsoever of him being detected. Mercifully, the guard's body language and ignorant manner told Snake he was in the clear for now.

However, about halfway across the dusty, hard and exposed ground, the guard stopped suddenly, holding in place, and he was looking Snake's way. Snake froze completely, hoping the darkness would cover him while the guard doubted what he may have seen. After about thirty agonisingly tense seconds, the guard began to move and looked the other way. Breathing a quiet sigh of relief, Snake moved faster to reach the fence without stopping again. He hadn't planned on almost blowing his cover before he was even inside the base, but luck was on his side tonight, so it seemed.

Inside the base...

Corporal Robert Flynn stood inside the guard rooms alone, preparing to go out on his shift. When he got the call from Mr Emmerich about a week ago, he was firstly incredibly surprised to hear that he was indeed alive, as he heard Shadow Moses was completely destroyed by a catastrophic accident with some of the warheads stored there, and that everyone was dead. He was even more surprised by the unusual request Emmerich confronted him with. To help an operative slip into the base and to provide them with intelligence on how to break into ArmsTech's remote system? He was tempted to refuse his request almost immediately, but Emmerich had swung him somewhat with the limited information he had provided about the operative's assignment. Stopping development of a weapon of mass destruction, which could be used on the US? He didn't know about anyone else, but Flynn did not want his wife and two children in their comfortable house in California being incinerated in a nuclear fireball.

Clearing the thoughts out of his head, he closed his locker, red cloth securely around his neck and very visible. Checking the safety and ammunition of his G36C assault rifle, he thumbed back the bolt, loading the first shot. If he needed to fire this weapon, the armour-piercing bullets in his gun that ArmsTech provided its entire security staff with would rip through Kevlar like it was tissue paper.

He didn't even feel the breathing of the man behind him as they slid the combat knife around and cut his throat in one swift movement.

His blood suddenly pouring over his front and staining his dark shirt darker, Corporal Flynn could only watch, dumbstruck, as he fell to the floor, choking on air as he died.

After the security guard's eyes became unfocused and glassy, the man with the knife relaxed a little. Grabbing the body, he pulled it up into the guard's locker, which was spacious enough to fit his body into. Taking off his balaclava, the man stopped a moment for some air. Holstering his knife, he pulled out his MP5 submachine gun, and mounted on it the silencer and laser-sight he had stored in his combat pack on his back.

Taking a minute to calm himself, the light showed that the left side of his face was scarred irreparably, as if something or someone had taken parallel chunks out of the flesh there. He had a crew cut, with a small but prominent scar running from his left eyebrow to above his ear. His right side then, was a severe contrast. Slightly blemished skin with only a few small marks here or there would allow someone to believe that his horrific injuries must have happened at the same time. Loading his gun, the man stood. Halting a moment, he stuck a Velcro patch onto the accompanying place on his arm.

The patch was a silver skull, elongated at the back with an eye patch, mounted on a black background.

Beneath the logo it said "_**Sons of Liberty**."_

The man moved to the far door that exited onto the compound proper, and moved into the darkness.

Outside, Snake had just broken through the fence. Rising up to a crouch, he drew his gun and moved over to behind a truck to keep out of the searchlights. Pressing his ear, he sent out a CODEC call.

"Otacon, I'm in." Snake said quietly.

_"Good work Snake! Now you need to find the corporal. If he isn't out on patrol, check the guardhouse."_ Otacon's voice crackled.

"Understood. I'm moving in now."

_"Oh and Snake?"_

"Yeah?"

_"Something isn't right about this place. Get that info ASAP and get out."_ The worry in Otacon's voice was unnerving, even to Snake.

"Okay Otacon, but don't worry about me. This'll be fine."

_"Good luck, Snake."_

Using the vehicles for cover, Snake began to move to one of the watchtowers in order to gain a better viewpoint over the base and find this man.


	4. Chapter 2: Conspiracies, Part I

**DISCLAIMER**

**Here's Chapter 4! Sorry for the delay (Christmas and all!) Enjoy!**

**MrStagg**

The spotlights swept across the ground, illuminating the areas they covered, but at the same time, making it much harder to see the area around the spotlight – they caused trouble with the guards' natural night vision. All Snake had to do was keep out of the beams, and in cover as an extra precaution, and he was practically invisible. Keeping low, Snake moved from vehicle to vehicle, passing around trucks, jeeps and armoured cars to get to the tall watchtower which was now around thirty metres in front of him.

Stopping a moment, Snake squinted slightly to see through the background glare of the tower's searchlight, to see if any guards were present in the tower. For little more than a second, he saw a faint blur of movement behind the light, and the reflection of light on gun metal.

_One guard, submachine gun. Looks like he is focused outside the tower instead of in. Good._

Snake had to get into the tower. However, just as he was about to move the truck parked immediately ahead and to his right rocked as someone got on board. Snake froze in place, not wanting to give himself away by being caught in the open if the truck moved. Sure enough, there was a small stutter before the engine rumbled to life, and the large truck moved off, down the main road out of the vehicle park and into the base proper.

Now left with thirty metres of land with no cover or shadowing, Snake had to move quickly to cross the area. As he was about to make his move, he stopped again. Over the sound of the general hubbub of the base, the faint scuff of footsteps over the gravel could be heard, gradually getting louder.

Snake, knowing what was about to happen, crouched down and remained still behind the truck. The door was opened and the truck wobbled as the soldier got in. Once that truck moved, Snake would be seen, unless he managed to make it across to the relative darkness of the concrete watchtower's door. When the engine started, Snake focused. Time seemed to slow down as his thoughts cleared, ever muscle primed, ready to start at precisely the right moment to move so as not to be seen or caught in the searchlights.

_Here goes nothing._

It was over in a matter of seconds. As the truck lurched forward from the throttle being pressed, Snake threw himself forwards like an athlete. Sprinting across the ground, his footsteps thudding and crunching on the gravel, he cleared the distance incredibly fast, a searchlight beam sweeping to the spot he was standing moments before, now in the open thanks to the truck trundling away right now.

Safely in the doorway, Snake caught his breath for a second or two before opening the door as quiet as possible, aiming his handgun around the room, checking every corner. The door clicking shut behind him, Snake looked up the metal stairways to the top of the tower.

_Shit, the angle isn't good here. Even so, I have to be ready. I will be climbing those stairs blind to what's up there._

The bottom of the tower clear, Snake climbed the stairs slowly and quietly, continually aiming his pistol at the opening to the top floor. As he neared the top, he breathed slowly and deeply.

_Just a quiet breach, then. There is only one lightly armed guard up there, but he mustn't hear me coming, or make a sound when I get him._

Moving slowly with a careful precision well-drilled into his mind and muscles, he climbed up to the opening so that he could see the top floor. It was a tiny space, and he saw the guard's boots and lower legs as they turned, quite by coincidence, to face the windows above the opening. The guard's eyes flicked over Snake momentarily, and even as he did a double take, his mouth opening in a expression of shock and total surprise, Snake was practically flying up the last of the stairs into the top level.

His fist connected with the guard's throat before he could cry out, the opening that provided allowing Snake to take the man's gun, CQC training long imprinted on Snake's mind taking over his body. As the gun left the man's hands, Snake's arm wrapped around his upper body from over the shoulder as he moved behind him. In seconds, Snake had the man in a powerful chokehold, his gun cocked and pointing at the side of the guard's head.

Coming off of his CQC-autopilot, as it were, Snake held the man tightly, their frenzied breathing and pure shock at what just happened to them preventing much of a struggle. Calming down from the immediate panic and noticing the cold barrel of the gun pointed at their temple, the guard stopped struggling, allowing Snake a moment to let out a calm, controlled breath and cast his eyes out of the nearest windows to check if anyone saw him. The base was as tranquil as it had been, which, although the flurry of activity made it difficult to discern any alarm, was hopefully a good sign.

_Since he is still conscious, I should interrogate him._

Half dragging the guard down the stairs, Snake stopped at the bottom, the man still tightly bound in the hold.

"Right, I can tell you aren't anyone more important than a security guard, and judging by your weight you're one of the donut-eating types." Snake growled into the man's ear, "but that doesn't make you useless to me, understand?" The man made muffled noises that almost definitely constituted a "yes".

"I'm looking for someone, Corporal Robert Flynn. Tell me where I would find him." Snake's tone was clearly threatening, in the kind of way that made you think if you didn't do what he said that this man would kill you as easily as he breathed. He loosened his hold slightly to allow the man to speak.

"Flynn... yes I can tell you where he is just don't hurt me!" The man whimpered pathetically.

"Tell me where he is!" Snake deliberately let some aggression slip into his voice to frighten the guard into talking.

"Okay, okay, please... Flynn should be on shift at the Western side of the base, near the storage units! Just please don't hurt me!" The man began to cry quietly.

_This is a member of ArmsTech's premier security staff? Crying like a baby in front of the enemy? Ha. They have got poor standards indeed._

"Thanks. Now I can't have you talk to anyone about my presence here..." Snake trailed off, the silence that followed hanging in the air like a death sentence.

"No no no please! I won't say a word!" The man sobbed, "Please don't hurt me! I can pay you, I-"

The butt of Snake's gun bashing into the side of his head knocked the man out cold. Chuckling somewhat, Snake dragged the guard's limp body into one of the lockers on the bottom floor and shut it.

_That was fun. Now to let Otacon know where we stand._

Opening up his CODEC channel, Snake connected to Otacon's frequency.

"Otacon, I interrogated a sentry and I know where Flynn should be."

_"Excellent work Snake, as usual! Where is Flynn?"_ Otacon sounded pleasantly surprised; no doubt because of Snake's fast intelligence-gathering.

"He should be somewhere close to the storage units," Snake responded "When I find him and talk to him I will call again."

_"Got it Snake. But before you go, I have some information of my own to share with you." _Otacon's tone had darkened suddenly, making Snake pay attention. _"While you were sneaking around I was eavesdropping on their communications channels as well as monitoring these fifty square miles by satellite. We may have a problem."_

Snake felt a small chill run over his body, that familiar feeling of the hairs on the back of his neck standing on end flowing through him. "What is it Otacon?" Snake asked quietly, his mind racing.

_"Something is wrong, Snake – very very wrong. There's a jammed frequency in the base's communications, normally a maintenance crew channel but if it were alright why block it? I followed the jamming signal to a small airfield about forty miles from here that is __**supposed**__ to be abandoned, however there are Blackhawk helicopters and lots of activity there." _The fear in his voice was the most disturbing detail.

"What's going on?" Snake asked quickly. He needed to know if the mission was compromised.

_"I think someone else is going to try and break in to the system, Snake. Thing is, these choppers look like backup, which to me means there may already be operatives inside the base. Watch your back, Snake."_ The last foreboding warning stayed inside Snake's head, almost echoing to him.

Snake now knew what the stakes were. He couldn't let anyone else get that information.

_Whenever someone other than us expresses interest in a Metal Gear, it usually isn't good. These guys sound equipped and prepared. If they get that data we're all dead._

Knowing that there was no time to waste, Snake crept out of the door.

_Western side, storage units. I have to find Flynn, and fast._

Snake moved into the darkness.


	5. Chapter 3: Conspiracies, Part II

**DISCLAIMER**

**Chapter 5 is up! I have no real time schedule for these but I write when I can, so I apologise for the irregular updating pattern. Anyway, enjoy!**

**MrStagg**

Sneaking across the base took around twenty minutes, according to Snake's watch as he checked it once he reached the storage areas. Around him were several hundred metres of shipping crates, storage buildings and stockpiles looming around him like a maze. Snake was confident that the guards present would not be patrolling each individual building or crate-lined alleyway, so as a result it was likely that Flynn could be found on the main route through the storage area, a wide dirt track that had supply trucks and jeeps continually traversing along its floodlit length, with foot guards patrolling along the sides and closest alleys. The majority of the area though, with small roads walled by shipping containers and small storage units, appeared to be deserted.

_This'll make my movement a bit easier, but the broken sight-lines will make it harder to spot Flynn._

Snake was hiding down a small alleyway, out of sight of the main road, watching from the shadows for a Flynn's red cloth.

_Damn it, there's nothing. I can't really see much of the main road from here anyway, so maybe I should get higher._

Looking up to his left, Snake saw that the containers were stacked in such a way that a person could climb up them. His eyes followed the vertical route to the top of the containers, some four storeys up, looking over most of the base and the main road.

_That would make a good vantage point, but I need to be careful. There is no cover up there so the longer I am up the more likely it is I will be spotted by the security crew. On top of that, the climb doesn't look like fun. But it's my best shot._

Moving to the opposite wall, Snake faced a meticulous climb to the top of the containers, starting with climbing the first, to which there was no leg-up or platform to stand on. Taking a deep breath, Snake ran at the container wall, placing his foot onto it, then the other, almost like running up it. Before gravity could pull him back down he threw out his arms and caught the top ledge of the container. Now hanging by his arms, he strained hard as he pulled himself up onto the top of the first storey.

_That went well. Now for the next three._

Thankfully, it turned out someone had left a small crate or two on top of each of the containers, allowing Snake a much easier climb up to the top. Once on top of the stacked containers, Snake realised he could see most of the base, at least until the large monolithic structure that was the compound's centrepiece blotted out the Eastern side from view. Lying prone, he crawled slowly to the edge of the container, so that he could look down on the road and the personnel on it.

Snake got out his binoculars and raised them to his eyes so he could see in detail despite the haze caused by the floodlights. Starting at the furthest Western edge by the perimeter fence proper, and sweeping along the road and up the other side towards the centre of the base, Snake watched carefully for Flynn's red neck-cloth.

_Nothing, nothing at all. I can't see it. If he isn't out on patrol when he is supposed to be, then where the hell is he?_

Snake called Otacon on his CODEC.

"Otacon, I can't find Flynn. I can't see him anywhere and this is his shift. Where could I find him?" The annoyance and exasperation filtered into Snake's tone before he could stop it, betraying his current feelings immediately.

_"What? He isn't there? Hell, Snake, if he isn't out there then..."_ Otacon trailed off, Snake already knowing what he would say.

"Where should I start looking?"

_"The guardhouse – should be about a hundred metres East, it's close to the central area by the HQ. Start there and then we will see about where to find him or what has happened to him. This is way too suspicious Snake. Be very careful."_

"Thanks Otacon. I'm moving out now."

Snake looked out from his vantage point and spotted a two-floor building just of the Eastern end of the road. A few guards were milling about the door, before another joined them and they walked off on shift.

_Looks like the place. Now to get to it._

As Snake climbed down into the pitch darkness of the shadows, the man lowered his own binoculars, watching from a guard tower some way along the fence. As he smiled to himself, the scarred half of his face twisting nightmarishly, he turned and walked down the stairs, past the slumped body of the sentry on duty, taking care to step around the growing pool of blood from the guard's slit throat.

Snake crossed over the road quickly and approached the door, the dim light above it making him momentarily visible before he slipped inside. With his gun drawn, he checked the isles of lockers and metal gun cabinets before lowering his weapon slightly.

_Clear. Not a soul in sight. That's good, but also bad._

Noting some cleaning materials and mop left nearby and a "wet floor" sign Snake concluded humorously that even on a top-secret base, janitorial staff were still needed to make the wheels turn smoothly.

Since it was obvious there was no one else in the guardhouse but him, Snake rested a moment, letting his mind calm somewhat. Pulling out a cigarette, he lit it and took a few long drags over a minute or two, calming his body. As he finished, he butted out the cigarette in the well-filled ashtray on a small table by the door, before thinking about what to do next.

_As a member of the security detail, he should have a locker around here. I should check it._

"Ah, ordered alphabetically, that should help a lot." Snake said quietly, his tone light despite the danger of his situation.

Moving along the rows of lockers, he found the one with a small metal plate with "FLYNN – R" written on it. Checking over his shoulder quickly, just in case, he turned to the locker and pulled the latch.

He was totally unprepared for the blood-soaked body that tumbled out of it, crashing on to him and knocking him to the floor.

"Shit!" He exclaimed quite loudly, throwing the body off of him and getting up quickly. Once his heart rate had calmed somewhat, Snake noticed that the dead guard was wearing a red cloth, now a deep brown, around his neck.

"Damn it!" Snake said to no-one in particular, his hands shaking slightly.

Flynn's shirt was saturated with blood, and there Snake noted there was a smooth cut across the man's throat, almost surgical in its precision, despite being performed by something obviously larger than a scalpel. Then he remembered the cleaning supplies.

Moving quick as a striking cobra, Snake pulled his gun out of its holster and aimed it around the room, his eyes flicking from place to place, watching for the smallest movement that would betray the position of the killer, if they were still here.

After he had decided that the area was clear, that it was just him and this body, he began to deduce the situation.

_Flynn must have been about to go on shift, but he was jumped. By the lack of signs of a struggle he was killed before he even knew what was going on._

Snake didn't really like that kind of kill, silent with no explanation. He preferred to sneak entirely and alert no-one or knock them out, not execute them like a hit man.

_The killer must have cleaned up what small mess there was, considering most got his shirt, and moved on. This is bad, he was my main ticket into the HQ plus it confirms Otacon's intruder theory. So now not only do I have to worry about completing the mission, I have to before this psychopath gets there or kills me. Great._

Snake spotted something else in the locker. It was Flynn's electronic key card, which granted access to the low-security sections of the base. He also picked up an assault rifle, a G36C, fully loaded with armour-piercing bullets and a few spare clips.

_Well his death won't have been entirely in vain. I now have more access and a suitable weapon to take on the enemy if things go South. Now to tell Otacon what's going on._

Snake pressed his CODEC.


	6. Chapter 4: Conspiracies, Part III

DISCLAIMER

**Here is Chapter 6! A full 1,000 words longer than usual, but then again this one is very important! Working on Chapter 7 now.**

**MrStagg**

_"What is it Snake?" _Otacon asked anxiously.

"I found Flynn, he's dead Otacon." Snake said sadly, almost sighing as he did so.

_"Oh no... Snake, that is very __**very **__bad news. How did he die, and what did you find out from the scene? Anything useful?" _Otacon said worriedly, trying to salvage the situation.

"His throat was slit cleanly, no struggle. Whoever killed him is clearly quite skilled at stealth, as well as equipped enough to ignore Flynn's gun, which I have now picked up. They also had enough time to clean up the mess."

_"Did he have his security card?"_

"Yeah, I got it on me now."

_"This is strange and very disconcerting, Snake. Whoever killed him must know you're here, and that you were meeting Flynn. But the question is how? And why leave his key card? Snake, I think someone must be onto us. They killed Flynn most likely to sabotage the mission but if so why leave a security card behind that can allow you to continue? Man, this is bad."_

"Yeah, tell me about it."

_"Do you want to pull the plug on the mission? I can be there in ten minutes."_

"No, Otacon. That isn't an option. We **_need_** the data, and we need to stop these guys, whoever they are, from getting it. I still have a job to do." Snake said, a recognisable determination, almost bordering stubbornness creeping into his tone.

_"Okay Snake. That key card won't get you into the HQ proper, but can get you access to the weapons testing and storage sub-basement almost directly beneath you. The entrance is outside."_

"Understood. Any information on what I can find inside?"

_"The sub-basement in question is three floors deep: Storage, Weapons Testing and Weapons Development. You will have access to the first two floors. Maybe one of the scientists or crew here can help you out? I'm sorry that it isn't much to go on but -"_

"Don't worry Otacon, I'll find something. I'm moving out."

Standing from the crouch he adopted while on CODEC, Snake glanced around the room quickly once more, just in case. Seeing no-one, he picked up Flynn's body and hid it back in the locker, so it couldn't compromise his mission.

He moved to the door at the other end of the building to the one he came in at, and leaned against the wall, taking a deep breath and clearing his head before he had to leave. Reaching to the door handle, he pulled it down so the door opened, and then let it swing free.

_Not a sound of alarm. Good._

He turned quickly and walked out of the doorway, back outside to the noise and movement of the base. Closing the door behind him, he crossed over the small road that was in front of him before crouching behind some wooden crates to prevent him being seen. In the relative dark created by being out of the glare from the road lights, he looked over the rim of the crate for any buildings resembling a basement entrance. In front of him stood the guardhouse, to his right a collection of crates and wooden pallets, but to his left there was a small building. Not large enough to be of any importance above ground, but it was the perfect size for an elevator and room to wait. Snake got up into a stooped walk, keeping low and moving fast. In a few seconds he was in front of the door. Checking over his shoulder he then opened the door and stepped inside.

The building's exterior would imply this is nothing other than a storage room, but the interior was a stark contrast to it. Where dull concrete and crates of equipment would be there was polished metal walls and bright ceiling lights. Engraved on the wall was ArmsTech's logo, an A engraved in a square, with "ARMSTECH" written above it. Snake recognised the logo from Moses – it was on Otacon's office computer during its start up sequence.

Ahead of him was a set of elevator doors, blank and unmarked. Above the door a small sign drew Snake's attention. It had a small picture of a stick man with a key card saying "1" on it. Snake pulled out Flynn's key card from a pouch and checked it.

_Level one security card. Good, that should get me in, at least._

Familiar with the function of key cards from Shadow Moses, Snake simply held it in his hand and walked towards the doors, which opened automatically. Once inside the elevator, he pressed the button for basement one, Storage. Immediately the elevator doors closed shut smoothly and the elevator moved quietly downwards, the machinery holding it almost impossible to hear. After about fifteen seconds, the elevator stopped moving, and Snake pulled out his pistol, ready to get out of the well-lit lift quickly and into cover.

As the doors opened wide enough for Snake to get out from, he slipped quietly and quickly out, and hid behind some crates, barely breathing so he could listen for any sound of suspicion or alarm.

_Nothing, phew. Now to see what I can find in this place._

Peeking up over the top of the crate, Snake took stock of the room. The storage area was well organised but apparently deserted. Not a soul in sight. The crates were generally low enough to allow sight lines, and in the approximate fifty metre-square room he couldn't see anyone at all.

_Alright, looks clear. Maybe I should search the area._

Standing up, with no fear of being spotted, Snake walked among the rows of crates, spotting boxes of guns, ammunition, grenades and explosives. Thinking on the spot, Snake found a box of C4 and detonators, and quickly armed and placed a charge in a small gap, surrounded by boxes of AA and AT rockets.

_This'll be a good distraction, and make one hell of a mess if I need to set it off._

Keeping a further four or so C4 charges, he kept walking around. He was about to check a crate that was strangely unmarked when he heard something.

The small noise of the elevator coming to a stop, and the doors opening.

Knowing that people were going to enter the room, Snake immediately ran to one of the far corners and hid a moment before looking out over the top of the large crate he was hidden behind. He saw four men in the elevator; one was talking to the other three. They didn't look like guards – they were wearing black combat gear, helmets and goggles. They had their weapons drawn and flashlights attached.

Realising these were some of the intruders, Snake pulled out his gun and touched his ear, trying to make a CODEC call. He couldn't get a response, and then realised that the signal was being jammed. Grunting in frustration he checked his ammo and thumbed off the safety.

_These guys want to take me down? They will be making the biggest mistake of their lives._

The fourth man, not wearing a helmet or mask, was visible to Snake for only a moment as the lift doors closed. Snake saw that one side of the man's face was horrifically disfigured. His refusal to wear a helmet implied he was more of an individual operator, most likely the mystery killer of Flynn, but Snake couldn't be sure yet. Either way, there were now three well-armed men, working as a team, between him and his exit.

He was going to have to go through them.

"We know he's here, the Colonel saw him go in. King's orders are to take him back alive." One of the men said to the others, his voice audible in the large space.

_Alive? Who is King? Who __**are**__ these guys? Well, if they want me alive, that will make my job easier._

Snake began to move. As the three men fanned out into a small triangle, two at the front and one at the back, Snake was flanking along the far side of the room. The men moved like they were trained in this kind of situation, holding formation with their weapons ready, checking every corner and side route as they walked straight down the middle.

_I need to draw them over to me, but keeping the element of surprise._

So Snake, moving parallel to the soldiers but about twenty metres to their side, stopped a moment and let one of his hands rest on the floor as he hid behind a crate, his arm almost clearly visible. The men were professionals, but they were underestimating him, still thinking they had the element of surprise on Snake. As they almost silently changed directions to head down to where Snake was baiting them, Snake moved away from the edge and sneaked away from his position, moving around the large amount of crates in a square. He was soon looking discreetly at the man taking up the rear of the group, less than ten metres away and directly behind them.

_I have to take him out first._

Readying his gun, Snake propped it lightly against the side of the crate, and aiming around the corner, lined up the soldier's leg in his sights. He began to squeeze the trigger, slowly applying pressure.

The soft "phut" noise his pistol made as the bullet spat out of the silencer was barely audible. Time almost seemed to slow down as Snake focused. The noises sounded dulled as the bullet punched through the soldier's knee, behind the kneepad he was wearing and shredding the joint before exiting messily out of the other side. As the soldier's eyes widened in surprise and he began to shout, Snake was already sprinting across the concrete floor towards the other two. Passing the other man's collapsing body, he grabbed one of the pairs' guns as they were levelled towards him, their shock and surprise making them lose their concentration. Wrenching the gun towards him and smacking the man in the throat with his forearm he stepped behind him and tripped the man to the ground, leaving one left.

The last soldier was stepping backward, his weapon already raised and finger on the trigger. Knowing that he didn't have enough time to reach him before he got shot, Snake sprinted to the side and jumped onto some of the crates. The soldier opened fire, his gun making a huge noise in the confined space, bullets whipping past Snake's head and body, embedding themselves in the ceiling above him.

_What happened to taking me alive?_

Snake was almost next to the man, as well as higher up. Jumping down, he crashed onto the soldier, pinning him to the floor, before hitting him in the face with the butt of his pistol, knocking the man out cold.

Looking around while breathing heavily, the adrenaline still pumping through his system, he picked the man he had tripped to interrogate, since the other one that was conscious was rolling on the floor, whimpering in pain at his damaged knee. Snake wrenched the man to his feet and pushed him against a crate, where he leaned, still breathing shallowly after the punch to the throat. Snake pulled out his pistol and pointed it right at the man's head, at point blank range.

"Why are you targeting me?" Snake asked menacingly.

_"My commander wanted you to be captured and taken to him, so he could finally meet you, as well as prevent you from stealing the Metal Gear information..." _The soldier wheezed, yet his dark eyes were fixed onto Snake's blue-grey ones. He was not afraid of him, Snake concluded.

"How do you know about Metal Gear and my mission?" Snake's tone was becoming urgent, rage taking over for a moment.

_"We have ways of gathering information that elude even your organisation, David."_ The man said quietly, the menace obvious in his eyes.

_Did he say David? What the hell? How does he know my name?_

Shocked and suddenly angry at the man's reply, Snake thumbed back the hammer on his gun and pressed the barrel into the soldier's face.

"How do you know my name!? Who the hell are you working for!?" Snake yelled at the man, but holding his gun alarmingly steady.

_"We know everything about you, Solid Snake. A military legend and hero, I do recall, not the terrorist you are now branded as. We know what happened at Moses, and we want Metal Gear." _The man said without a hint of shame or emotion in his voice other than malicious glee.

"What do you mean, we?"

_"The Sons of Liberty, and our leader, of course."_

"Sons of Liberty? Are you some kind of PMC?"

_"We are much more than a mere PMC, Snake. We are the future. And the King wanted to meet you, face to face."_

"I didn't realise Elvis was with you," Snake chuckled humourlessly, "can I have an autograph?" he asked as he hit the man in the face with his gun, knocking him out.

As the man slumped to the floor, Snake turned and knocked the last one out too. In one of their body armour pouches he found some cable-ties and high tensile cord. In a few minutes, all three men, one of whom was snoring contentedly, were trussed and tied, hidden in one of the large boxes in the room.

_That should be the last I see of these guys for a while, at least. Now to close up._

As Snake lifted up the lid of the box to place it over the three unconscious men, he stopped suddenly, his eye catching something that threw his whole world out of its comfort zone.

On one of the men's arms was a patch, on it was a symbol. The silver eye patch-wearing skull.

_It can't be... Big Boss?_

Unwanted memories assaulted Snake's mind: the horror of discovering that Big Boss, the leader of FOXHOUND, was responsible for constructing Outer Heaven, a mercenary nation of incredible power, and the first known incarnation of Metal Gear? The pain of fighting the Legendary Soldier, and again in Zanzibarland a few years later. The screaming he made as he was burned alive by Snake's makeshift flamethrower. All the fury, all the pain and all the sorrow of that troubled, flawed man, fighting for endless worldwide warfare, a world where soldiers would always have a place. Snake felt again the sense of loss when he had killed him, and lastly the confusion and anger of discovering a year ago that he was Snake and Liquid's biological father.

Big Boss was dead. Snake was sure of that, particularly since his body was in US hands. But how, then, could these men be walking around wearing his symbol? Snake had no doubt that "King" was the leader of these "Sons of Liberty", but if it wasn't Big Boss, then who?

_Who indeed._


	7. Chapter 5: Recruitment

**DISCLAIMER**

**Here's Chapter 7! I am sorry for the delay, but I have some exams coming up and my schedule has been pinned down. Unfortunately this may mean no more updates until after January 25th. Sorry readers! I will try and work on Chapter 8 when I can.**

**MrStagg**

Checking the box was securely shut, Snake turned and walked towards the lift.

_I still have a job to do, intruders or not. I need to find a way into the HQ and into the mainframe. Until I have that data, everything else is secondary to my mission._

As the lift doors closed behind him, Snake pressed the button for "Weapons Testing": sub-basement 2.

_Hopefully I can find a scientist, researcher or technician, hell __**anyone**__ at all who can help me out._

When the doors opened almost silently, Snake left his thinking-time and looked around. Ahead of him was a long corridor, stretching about fifty metres, so it was similar in length to the storage room above it. However, whereas the storage room was open, testing rooms were each behind numbered glass doors running from one to twelve. Quiet activity could be heard inside.

_Looks like the offices at Shadow Moses. Ha. No electrified floor this time though. At least I know there's someone in here with me._

Snake paused a moment in remembrance. On the way to rescue ArmsTech's CEO, who was a hostage to Liquid, he encountered a room with electrified floor. He still needed to get across so he used a Nikita remote-control missile to fly through the office corridors to his the power box in the utility room. Then he fought Revolver Ocelot, the Russian torture specialist, in a room wired with C4. And Gray Fox...

_Focus, Snake. Gray Fox is dead. You have a job to do._

Drawing his gun, Snake moved slowly and silently, his weapon raised and finger on the trigger, ready to kill at a moment's notice – the threat of the mystery infiltrators and the needless death of his informant were beginning to weigh on his mind. Door one was approaching on his left, and so with his back against the wall he crept up to the edge, peeking around to see what was inside.

Snake could see just one man, in a white coat, with something that looked like an elaborate rocket launcher on stands on a metal table in front of him that he was fiddling with, wires and metal panels strewn over its surface. Glad to see that this time there was only one guy, Snake opened the door quietly, creeping up on the man who was clearly so engrossed in his work that he couldn't hear him at all.

Snake crept up right behind the scientist, a thin, short man, with average sized blonde hair. Pressing the cold muzzle of his gun into the back of the scientist's head, the man instantly froze up, becoming very aware of his danger.

"Listen to me carefully. I need a way into the HQ and the mainframe. Tell me how or point me to someone who can or I will kill you." Snake hissed into his ear menacingly, his tone illustrating his conviction, and that the threat was very real.

"Okay okay! If you were looking for a way in I can tell you how." The man said fearfully.

"Tell me and I will let you live."

Although Snake wasn't going to shoot the guy, he did try his hardest make it sound like he would.

_Otacon was just like this guy when I found him in that locker back at Moses. He's innocent._

"Hurry up!" Snake snapped.

"Alright, alright, just for the love of God don't shoot!" The man pleaded.

"I won't if you talk." Snake let the threat hang.

"Okay, okay. The mainframe is housed on the fourth floor of the HQ building, and is only accessible from the secure elevator in the lobby. No stops, it just heads right up. The mainframe room, in particular, is protected by an automated defence system."

"Defence system?"

_This could be trouble._

"Yes, I don't know the details other than that you need the biometric data of one of the staff authorised to enter it with you at the time. The system makes no exceptions." The man desperately tried to lie, and for the moment succeeded.

"Who's authorised access?"

"Well, me, for one."

"You? Why then, are you out here working on weapons and not somewhere more secure?" Snake was surprised to hear that this seemingly ordinary scientist was of any importance at all. "Just who are you anyway?"

"I am the Chief Engineer, William Orson. I have access to the mainframe. But why do you need me?" He asked.

_I think it's best to let Otacon fill this guy in._

"Do you have a CODEC device?" Snake asked quickly.

"Yes, all of the senior staff members have them. Why?" The engineer responded with suspicion in his voice.

"My operator can talk you through the rough information," Said Snake, as he holstered his weapon. "They key point here is that I need your help. I would prefer to have it willingly."

"I understand," Orson replied, his eyes following the gun to Snake's holster before he relaxed somewhat. "What frequency?"

"141.42."

Orson nodded, and pressed his fingers to his ear. While Otacon explained to Orson what was going on, which would take a few minutes by his reckoning, Snake walked out into the corridor, drawing his pistol and standing in a stable shooting position. He had to clear out the rest of the rooms.

Over the course of about four tense minutes of checking each door and room, Snake walked back to room one, having only found mysteriously vacant tools and work areas.

_No-one else here, none at all. Not even a guard. This is unnerving; I should probably ask Orson what's going on._

As Snake returned to room one, Orson was standing up. Before Snake could say anything, Orson turned to him.

"You friend Emmerich explained the situation. I'm in." He said, his voice full of determination.

"Really? You're sure?" Snake was surprised and pleased that Otacon had convinced Orson to join up.

"Yes, Snake. Emmerich let me know the stakes. And as you probably guessed I lied to you about my knowledge of the security systems. I know everything about them. After all, I designed them." Orson said the last part with a hint of disgust.

"Why?"

"I was scared. Sorry."

"It's alright Orson; just don't lie to me again." Snake said.

"I won't. We need to make a stop off a floor below to retrieve my access card. It needs scanning as an extra feature of the mainframe security."

"Lead the way."

As they stepped out into the corridor, Orson stopped in place, looking around the room.

"What is it?" Snake asked, his mind already putting together the pieces.

_No guards. No-one._

"Well, where is everyone? Did you knock them out?" Orson asked, turning to Snake. Seeing the blank look on Snake's grizzled features, Orson put two and two together, and his face drained of colour.

"Oh my God, the people who you encountered earlier must have taken everyone! I didn't even notice! Where could they have gone?" Orson said, the fear in his voice evident.

"Calm down! I need you not to panic. We need the access card, Orson." Snake said firmly.

_If they could get everyone, why leave Orson?_

"Okay, okay. Well then, we should move on." Orson and Snake walked into the elevator, the engineer pressing the button for the "Weapons Labs", sub-basement 3. The elevator system detected Orson's nanomachines and the doors closed smoothly.


	8. Chapter 6: Backup

**DISCLAIMER**

**Here's a mini-chapter I was working on, readers! My schedule isn't as pressured as I had feared so I may yet be able to upload Chapter 9 before the 25th.**

**MrStagg**

The day was beginning to lighten, if only a little. The darkness of the security room remained, however, obscuring the five dead bodies lying in their chairs or on the floor, one with a slit throat, and the others with gunshot wounds. The man was watching one of the CCTV monitors intently, the one covering the Weapons Labs elevator. He saw the head tech standing in it with the man he was looking for.

Solid Snake...

The man's green eyes were almost burning through the glass of the screen in anger. His left hand twitched, as it always did when he was angry. He reached up and ran his hand along the horrific scars that encompassed the side of his face.

He pressed his hand to the communications earpiece he was wearing. Almost immediately, the voice on the other end was asking about their progress.

"He's a little behind schedule, but the teams won't need to wait," He growled, his voice like a saw through bone, "He incapacitated the capture crew, as expected. For one man, he is particularly skilled."

The voice blared in his ear angrily.

"Yes sir, sorry sir. They should be out soon and onwards to the HQ. I will already be inside by the time they arrive," He said, a malicious smile playing at the corners of his mouth, "And what of the tech? Orson is now his accomplice, what use will he be to us?"

More sound assaulted his ear.

"Understood, King. I will extract what I can and dispose of him. When are the forces coming in?"

**40 miles away...**

"0330. You know the price of failure, Colonel." The man shut down his communications device and turned to the sergeant next to him.

"We are wheels up sergeant. Get the men on to their choppers and move out."

The soldier, clad in all-black combat gear, aside from the Sons of Liberty patch on his arm, nodded and left the room. Standing on his own in the airfield's control tower, the man checked the sword he kept strapped to his back in its carbon-fibre scabbard.

_Still sharp, good._

Loading his gun, a Belgian P90 submachine gun, he turned and walked to the door, the lights showing the features of an ageing man, with white hair and beard, grey eyes and an authoritative figure.

Walking outside to the landing strip, the Sons of Liberty's strike team was already mounting the Blackhawk helicopters. King approached the Sikorsky MH-53 helicopter, known to the men as a "Pave Low", the roar of the rotors deafening.

Once on board, he switched on the radio device that would transmit to all of the soldiers in the strike force.

"The journey is 40 miles, gentlemen. Lock and load. I want full fire coverage as we arrive. If we take them by surprise, this will be simple. For Liberty."

Signing off, he waved his hand and gave the signal for liftoff. As the helicopters pulled away from the ground and began to fly to the base.


	9. Chapter 7: Suspicions

**DISCLAIMER**

**Here's Chapter 9! I will not be uploading any more until after January 25th, but hopefully this will suffice for now!**

**MrStagg**

Snake stepped out of the building into the fresh night air of the base, Orson following almost immediately. Snake had his pistol ready, checking down the paths either side of the door.

_Clear._

The trip to Weapons Development was a short one, but somewhat more unnerving than the Testing department. Once again, there was no-one in sight, but this time there looked like there was a struggle. Tables were overturned in the expanse of the hall, workstations disrupted and computers destroyed. Most worrying of all was the presence of blood and shell casings, which led Snake to believe that these "Sons of Liberty" were not interested in the wellbeing of the ArmsTech personnel.

Snake, remembering his pickup was at 0530, checked the glow-in-the-dark diving watch he wore.

_0310. Still some time left._

Snake motioned to Orson over his shoulder to follow him closely.

"Do as I do, Orson. Follow my movements and obey any order I give you. Understand?" Snake said firmly.

Orson nodded, his nerves on edge.

As they moved off, past crates and vehicles, they began to close on the looming structure of the HQ, a four-floor concrete building with relatively large windows. It could be mistaken for an eighties office building. Snake knew it was anything but.

Before long they were running along the edge of the building, keeping low. Snake checked the time again.

_0315._

Spotting a gap in the extensive lighting over the road that ran past the HQ, Snake and Orson ran over the road in the darkness, moving to a position whereby they could see the entrance to the HQ.

Crouching behind a concrete block, Snake peeked over the top, his bandana fluttering lightly in the heightening winds. Due to the slowly changing weather, just as Otacon had predicted, dust was beginning to fly. It was a little at the moment, but could grow into an impenetrable wall of sand over a matter of minutes.

Looking over at the door, Snake saw two guards standing vigilantly in front of the two glass doors that made up the main entrance to the building.

_Damn. How do we get past those guards?_

"Orson. We need to get inside, do you have any ideas?" Said Snake as he turned to face his white-coated counterpart.

"I could go up and ask to be let in, maybe that can distract them enough for you to get close." Said Orson, and despite his nervousness he was showing a remarkable ability to keep his cool in situations like this.

_He and Otacon really are of the same mould._

"Okay, well you need to keep their attention long enough for me to get to them. Can you do that?"

"Yes."

Snake nodded to Orson, who moved out of the sight of the door guards and began to approach along the road looking as convincing as possible. Moving with confidence, he walked into the glare of the lights above the door, the guards noticing him instantly, tensing and then relaxing, obviously recognising him.

_Good. Now to move._

As Orson chatted with the door guards, keeping their attention, Snake crossed the road and approached along the wall of the building, in the peripheral vision of the nearest guard, who was thankfully distracted by Orson's conversation. Orson knew Snake was approaching, but for a moment lost his train of thought in the conversation.

_Crap._

Snake gave up all pretence of stealth at this point and sprinted the short distance to the first guard, who was turning to meet him with a shocked expression. As Snake tore the man's gun away and flipped him to the floor, he didn't notice that Orson had pulled a revolver out of his jacket and was pointing it at the other guard's face, his aim unflinchingly steady.

"Drop the gun. If you don't I will shoot you." Said Orson, his voice held steady and threatening. The guard lowered his weapon and put his hands on his head, at which point Orson whacked him over the head with the butt of the revolver, knocking him out.

Snake was surprised and shocked that Orson was proficient in the use of weapons and capable of such a controlled explosion of violence, with intent. He had underestimated, and as it seemed, forgotten to search him.

_I must be losing my touch, missing these details._

As Orson tucked the revolver, a .357 Magnum, into his coat, Snake turned to him.

"That was impressive, Orson. How did you know how to fight like that?"

Orson shrugged, "Standard ArmsTech policy. I'm not a huge fan of violence, and despise the use of technology to kill, like your friend Otacon. I much prefer to help people, or at least provide security to the warring nations of this world. I don't care much for killing ordinary people", he said nonchalantly.

"Works for me. Can you get us inside?" Asked Snake, gesturing to the scanning device stuck to a panel by the door.

"Of course."

Orson walked over to the scanner and presented his ID key card to the scanner. After a few tense seconds it beeped and the doors clicked unlocked. Motioning to Snake to follow, Orson walked calmly through the doors and into the lobby of the HQ.

While the rest of the base was of a sparse military nature, the HQ was a total contrast. Shiny linoleum floors and wood panelling on the walls were well lit by illuminating lights along them, presenting, rather than a top-secret military installation a businesslike formal interior. Snake half expected for there to be men in suits hurrying around like the general corporate stereotype. This lobby, however, was completely deserted and dead quiet.

"Strange," said Orson, "there's supposed to be a receptionist and some security staff at least."

Snake, realising that all was definitely not as it seemed, pulled out his unused G36C, thumbing off the safety and checking the chamber. He was taking no chances now.

_How come the guards didn't notice the absence of staff inside?_

As Snake realised the door guards were impostors, he sprinted back to the entrance, only to see that the unconscious bodies had vanished, and that the doors were locked.

"Orson!" Snake said, trying to pull the handle on the door to no avail, "the doors have locked!"

Orson turned and ran over to Snake, pressing his card against the scanner.

The light stayed red.

_Shit. We're trapped in here, and definitely not alone._

Snake wanted to call Otacon, but he wasn't safe, and neither was Orson. As he turned away from the door once again facing the quiet lobby, he raised his gun and began to walk, his finger on the trigger and ready to fire.

"Orson, better get out that gun of yours."

He nodded and reached into his coat, pulling out the revolver.

"Stick close. I don't know who's in here with us."

Orson watched Snake's back as they peeled off down the left of the two corridors, one on each side of the lobby. Snake was following the signs labelled "Security Office", his eyes flicking from door to door as they passed them.

_All quiet._

As they turned yet another corner, after about five minutes, Snake spotted a door at the end of the corridor, a sign above marking it as the Security Office. Moving much more slowly now, and absolutely quietly, Snake crept forwards, his aim not moving from the door. As he approached, he saw that the normal keypad lock was smashed, and that the door itself had been broken.

Snake reached out for the door, his gun still raised, and placed his hand on the handle.

_Guess all that practise breaching doors is about to pay off._

Snake threw open the door and stormed through, aiming his gun quickly to each of the four corners of the room, checking them and finding them empty. As he lowered his gun, he realised what was in here.

Five dead bodies were sprawled out in a myriad of positions across the room. One was in its chair but the others were lying over the security consoles or floor. As he walked over to the first body, taking care to avoid the blood-saturated parts of the carpet, he saw that the man's neck was slit fully.

_Just like Flynn._

Looking around, Snake deduced that the attacker had slit the throat of one, and shot the other four as they became alerted, hence the mess and strange positions.

"Oh my God..." whispered Orson, frozen in shock and horror.

"They must have been watching us" said Snake, gesturing to the CCTV monitors that covered the weapons labs and elevator.

"No alarm was raised."

"Then that means these men were already dead."

"And, as I recall correctly, we are stuck in this building, _with_ these maniacs?" Said Orson, beginning to panic.

"Calm down! They can't sneak up on us if we work together" said Snake.

Snake looked at the CCTV cameras for the rest of the base. At the same time, he heard some helicopters flying around in the distance.

_Probably another delivery for these guys._

Snake checked his watch.

_0330._

Snake heard a few small "crump" noises in the distance through the windows of the room.

_Is that gunfire?_

Almost immediately after, Snake looked back at the monitors to see a massive amount of activity. The black and white footage was poor quality but Snake could clearly see guards running left right and centre as they were gunned down from above. Then the explosions started. A roaring noise accompanied by a loud boom announced the arrival of these new attackers – Snake ran to the window.

Looking out he could see the base's staff facilities collapse in a fireball, glass shards and lumps of concrete exploding outwards in all directions as the building crumpled under its weight. Above, blasting a bright light over the ground was a massive helicopter, the guns on the sides firing indiscriminately at the personnel nearby.

Rockets were being fired from other helicopters, despite being out of sight to Snake. As the base's alarm system began to blare, a whine going up and down in pitch repeatedly, all hell really did break loose.


	10. Chapter 8: Plans

**DISCLAIMER**

**Here's a mini-chapter for you while I work on the next major part! Chapter 11 is on its way!**

**MrStagg**

"Damn!" Yelled Snake, checking his G36C.

_Loaded, round in the chamber. Three spare clips, armour-piercing. This'll have to do._

"What's going on?" Orson shouted, the roar of noise and activity forcing him to raise his voice.

"Someone's attacking the base!" Snake said, already forming a plan and remembering the massive helicopter he saw just earlier.

_I have to take out their leader. That should provide me and Orson the time we need to get into the mainframe._

"I have to go out there," Snake said, his growl barely audible over the explosions and gunfire, the helicopters' rotors breaking up the sound with each rotation. "We can't let them take over the base, we won't have the time we need to complete the mission! This is the only way..."

Orson nodded. "I'll stay here, Snake! I can take care of myself for a few minutes."

Before he left, Snake remembered the C4 he had planted in the weapons labs, and the charges he was carrying. A plan in mind, he handed over the detonator for the armed C4 in the storage area.

"Orson, this is a detonator for C4 that I placed inside the weapons storage, next to enough explosives to flatten all three floors of the structure. If these guys come searching in here for equipment, or in enough numbers, blow it all up."

Orson held the detonator carefully in his hand, as if it would go off at the slightest touch.

Turning without another word, Snake sprinted out into the corridors, following the signs for the lobby, his combat boots thumping on the floor. He turned into the lobby, still as deserted as it was earlier. Snake approached the door, aiming a solid kick at the lock. Swinging with all his might, his boot connected with the force to crush an ordinary lock. The door, however, didn't budge.

Swearing loudly, Snake aimed his rifle at the lock, and squeezed the trigger. A short burst of deafening shots was all he needed to shatter the lock and the doors to swing open. Snake ran outside.

As he went outside the wind caused by the helicopters hit him full in the face. He could feel the heat from the fires burning away nearby, and smell the gunpowder in the air. If he thought it was loud inside the building, outside was a veritable cacophony of noise. The explosions, gunfire, the whine of the alarm and the "whup-whup" sound of the helicopter rotors was deafening.

Knowing that he didn't have much time, Snake steeled himself and ran out into the smoke.


	11. Chapter 9: Heat

**DISCLAIMER**

**Here is Chapter 11! Hope you all enjoy. I apologise for the delay but life issues and a sudden loss of direction with this fic have taken their toll on my work. I should be uploading Chapter 12 soon though!**

**MrStagg**

Snake was breathing heavily. The running from shadow to shadow all the while listening and watching for enemies to avoid detection was taking its toll. He had been on the move for the better part of a few minutes and had seen that these "Sons of Liberty" were quickly taking over the base. Sporadic gunfire was still all around, and combat teams dressed in all-black were beginning to fan out through the area, searching for any personnel and as Snake increasingly started to believe, him also.

Turning a corner with his G36C raised, he checked the small alleyway between the shipping containers was clear before lowering his gun and leaning against the wall of one, catching his breath. The sound of the helicopters and base alarms were still loud, but almost deadened as Snake rested in the dark.

Despite the stress of the situation, Snake knew that he never felt more alive than when he was in war.

_Better._

Feeling a little more refreshed after his breather, Snake stood straight and began to move. However, as he leant against the corner wall, ready to jump out, he hesitated.

Suddenly much louder than before, helicopter rotors were approaching. As Snake looked above, the alley was blazed with light as the Pave Low flew overhead, its machine guns firing randomly into the surrounding area.

_That's the one. I need to take it down, and fast._

The helicopter flew overhead before disappearing behind a building, the medical centre to be precise. Checking out into the road between him and the building, and seeing that it was clear, Snake sprinted from his cover and over to the wall of the building. The sound of the Pave Low's rotors had not deadened.

_They're staying still. Now I need something to take it out with._

Snake turned out around the edge of the building, and ahead he could see the massive helicopter hovering in place, its rotors kicking up a huge cloud of dust and gravel over the makeshift helipad it was currently hovering over. Just as he was about to move away from the building to find a weapon, though, Snake saw blurry shapes in the dust cloud.

_Soldiers._

Without stopping to think, Snake sprinted out into the dust, off to the side of the furthest-out silhouette. Sure enough, men in combat armour wearing "Sons of Liberty" patches were moving in formation to the spot where Snake was less than ten seconds ago. The formation the soldiers were standing in caused their line to be at an angle, so one man was at the back and behind the others.

_Perfect._

As Snake stalked the man through the dust cloud, he raised his gun, knowing that if the man cleared the disturbed dust and sand he would have no choice but to open fire on all of them.

Snake was drawing closer; the back of the soldier was almost within reach.

_Now!_

Running behind the man and knocking his gun away, Snake used him as a human shield while he opened fire on the other four one-handed, his bullets still remarkably accurate. Controlling the recoil from the G36C, the spent shells flew past Snake's head as he emptied the clip at the soldiers. The men were turning in shock and alarm as the AP bullets punched into their armour and through it, blood spraying out of their ruptured skin. As the last man fell, Snake's gun clicked empty.

Snake knocked out the one he was using as a human shield with a solid blow to the head, just as he noticed the helicopter flying a little higher, no doubt to let the dust clear. Snake sprinted away to the side as the dust cleared, now safely crouched behind a concrete barrier.

**Inside the helicopter...**

The aged man looked out of the window, seeing the men being covered up by the cloud of dust caused by the helicopter, grunting in displeasure.

_These things always make visibility bad._

As he was about to turn away, he saw something out of the corner of his eye. A blurry shape, gone before he knew it was there. And suddenly he saw flashes in the cloud.

_Gunfire!?_

Turning to face the cockpit, he roared down to the pilot "Get us up! Now!"

Almost immediately the helicopter began to lift, the cloud beginning to clear. Looking out of the window again, he saw what was left.

In a matter of seconds **_he_**had taken out an entire squad, and was gone before he could have been spotted.

_Truly masterful, but I guess that's how any clone of him will perform. There is nothing we can do here._

Turning again to the cockpit, he said to the pilot "Take me to the HQ building! We can wait for him there."

The helicopter lifted away and flew in the direction of the HQ.

The man looked out of the window at the corpses of his men, and at the fires and other helicopters across the base. At that moment, his hatred of Solid Snake was absolute.

_I am the boss to surpass Big Boss himself. There will be no impostors._

**On the ground...**

_I still need something to destroy that thing with._

Dropping into a crawl and keeping out of visibility Snake moved slowly towards a road that he knew would take him to the motor pool. Out of the corner of his eye he saw the helicopter lift off completely and fly towards the HQ building.

After a minute or so had passed, Snake was creeping slowly along some shipping containers before he turned towards the vehicle park, and stopped suddenly.

_Well, this wasn't what I had in mind but I think it'll do._

In front of him was an M1 Abrams tank, abandoned in the middle of the road. The bodies slumped over the sides led Snake to believe that it had been stormed by the Sons of Liberty and the crew taken out and killed. But he didn't need a crew anyway. Smiling slightly, Snake ran over to the tank and climbed up to the top, opening the hatch and dropping inside. Closing the hatch behind him he transferred into the driver's seat, noticing a computer monitor to his right and the observation slit to his front in this cramped space.

Checking the screen, the Tank was already on, but the engine had been switched off. Snake knew how to operate one of these. After all, he had served in the US Army before FOXHOUND, so he was proficient in the use of many pieces of military hardware.

Snake pressed the ignition button, the 1500 horsepower gas turbine engine roaring to life as the tank began to shudder slightly under the seat. Checking that the essential systems were working, Snake placed his hands on the track control levers to either side and his feet to the pedals beneath. Pressing forward with his hands, the tank blasted forwards.

Snake remembered the route to the HQ building, where he assumed the command helicopter was still waiting.

_Let's get to work._

The tank roared off down the road, already pushing 30 kilometres an hour.


	12. Chapter 10: Identities Revealed, Part I

**DISCLAIMER**

**Hello again, readers! I apologise sincerely for my absence, I understand that several of you were looking forward to an update and how annoying it can be when the author doesn't update for about 3 weeks! Alas, personal problems got in the way and I have now completed a relatively short Chapter 12 for your enjoyment, as the story works towards its concluding section.**

**Thanks,**

**MrStagg**

The tank barrelled along the sand and gravel roads, the tracks whirring and the engine roaring. Inside, Snake was being shaken back and forth.

_I always hated the suspension in these things._

Gunning the throttle a little further, Snake saw in the optic display that the sky was beginning to lighten. Given another two hours tops, it would be dawn. And dawn brings trouble. As the HQ area was coming into view, Snake pressed his CODEC to call Orson.

Orson's shaking voice crackled over into Snake's ear. _"Snake, what is it? I'm still alone at the moment, but I don't think I can hide here much longer. Hurry." _The fear in his tone was unmistakeable.

"Relax Orson; I'm on my way back now. Do you still have the detonator I gave you?" Snake asked him quickly.

_"Yes."_

"Press it." Snake said calmly, aware that the destruction the bomb would cause would provide a big enough distraction to let him take their leader down.

Over in the HQ, Orson's hands were shaking. The sweat was pouring off of his forehead, and his breathing was ragged. He wasn't sure of the last time he had been this stressed.

_Just press it!_

Orson steeled some resolve, and after a short pause, clicked the button.

What followed was destruction on an incredible scale. The first thing anyone heard was a sudden "krump" noise followed immediately by a titanic explosion, the shockwaves shattering windows a hundred and fifty metres away. Soldiers stood dumbstruck, others running as the desert earth blasted upwards combined with chunks of concrete and metal in a fireball more than fifty feet high. The resulting blast knocked shipping crates onto their sides, causing piles of them to come crashing down in a cacophony of scraping and screeching metal. As the destruction radiated outwards, the smoke from the munitions spread, the pieces of earth and what was left of the weapons basements raining down over the ground. As the explosion expanded, a relative silence fell over the base, even the helicopters, with their missiles and miniguns appearing quiet.

Snake slammed into his seat as the shockwave hit the back of the tank, slowing it to a halt.

_Ha, that was impressive. Makes me want to do it again._

As Snake sped up again, the HQ came into sight. And sure enough, as he had predicted, the large helicopter was hovering there, its rotors thumping in the air, spotlights gleaming. Snake stopped as soon as the tank was in the open, then darted out of his seat and climbed into the gunner's seat.

The old man was stunned when the shockwave made the helicopter wobble in the air, his mouth dropping open slightly at the monstrous explosion sending light and debris into the sky, fire raining onto everything in the blast radius. Then, as a minute ticked by in sudden silence, he turned to see a tank parked in full view of the helicopter, the 105mm cannon aimed right at it.

_See you in hell._

Snake rammed the shell into the loader, the barrel closing with a satisfying clunk, before climbing quickly back into the gunner seat, and checking the aim.

The fuzzy computer display had the helicopter right in the middle of the screen, the symbols for firing lit green. As Snake thumbed the control, he saw through an open port in the side of the helicopter an old man, grey haired and imposing.

He froze as the man's features became clear to him, just for a moment. Memories assaulted his thoughts, his hand hovering over the button...

...Snake was running, bullets flying past his body, as Big Boss stood, machinegun in hand, fighting him to the end. He remembered pain, and heat, and the way Big Boss screamed in agony as he burned alive from Snake's makeshift flamethrower. He remembered his speech...

_"Whoever wins, our battle does not end. The loser is free from the battlefield, but the winner must remain there and the survivor must live his life as a warrior until he dies."_

...he remembered the feeling of loss and sorrow when he left that place for good. He remembered...

_...It can't be! Not him!_

"Enough!" Snake yelled, as his thumb slammed down on the fire button.

The tank lurched as the shell exploded out of the barrel, a split second going past as the shell tore through the side of the fuselage and out through the roof, shredding one of the engines and the rotors.

As the helicopter exploded in a roaring fireball, shrapnel blasting outwards as the fuel caught fire, Snake thought he saw something.

The silhouette of a man, jumping from the helicopter as its carcass landed with a screeching, crunching noise on the ground and exploded.

But as soon as it was there it was gone. Snake pushed it out of his mind. He observed the carnage. No-one could have survived that.

Climbing out of the tank, Snake dropped onto the dusty ground, flames blazing all around. Readying his gun, Snake ran through past the wreckage and over the entrance of the HQ, where the doors were almost entirely blown off, the concrete blackened and chipped. Going inside, he decided to regroup with Orson and get to the mainframe.

Watching him go inside, the old man stood from his hiding spot, his combat uniform torn and singed. He smiled, but it was a hard, cruel one that did not reach his eyes, which were glinting with malice and hatred. He started talking into his earpiece.

"He's gone in. Colonel, draw him to where we need him."

Quickly changing to the general channel, he spoke again. "Attention all units outside of the HQ building, this is King. Regroup at the wreckage of the Pave Low. Let's finish this."

Lowering his hand, he suddenly fell against a shipping container and took a deep breath, his old body betraying him momentarily.

"Damn them. Damn them all." His voice seethed with anger as he righted himself. He could hear the troops inbound. It would not be long.


	13. Chapter 11: Identities Revealed, Part II

**DISCLAIMER**

**Hello all, sorry for the delay. Here's the penultimate chapter in the story. I will endeavour to finish everything up soon, and as always feedback is appreciated. On a side note, I came up with an idea for a new fic, written from the point of view of some MSF soldiers working for Big Boss in the 1970s, in Southeast Asia. Would this be something you would want to see? PM me with your opinions, if you could.**

**MrStagg**

Snake padded along the deserted corridor, the lights flickering from the damage done to the base's generators. The shadows cast Snake into darkness, his grey eyes piercing his surroundings, looking for any sign of the enemy. As he neared the security office, he slowed down, raising his rifle and moving silently. Casting his eyes about the corridor, he began to creep forwards.

_No-one. But it's too quiet._

Snake pressed himself against the doorframe, before jumping out around the corner, weapon aimed into the room.

"Orson!" Snake hissed, "Are you there?"

_No reply._

Stepping into the room, Snake looked over to where he told Orson to hide. A small dark stain was visible on the floor.

_Blood..._

Snake stopped, realising now that Orson was in the hands of the Sons of Liberty.

_The mainframe. I've got to stop them._

Casting all notion of stealth out of the window, Snake ran down the dark corridor further into the building, following the signs for the mainframe express elevator. His footsteps thumped on the fake marble flooring as he ran, his bandana trails flapping behind his head.

However, as Snake got close to a turn, not far from the elevator, he saw a lighter part of the hallway.

_Flashlights._

Almost on cue, the lights fully flickered out, plunging the entire corridor into darkness.

Snake pressed against the wall, and carefully leaned around the corner. Ahead of him were about fourteen soldiers, armed to the teeth, equipped with flashlights and all guarding one room. The elevator room was more like the building's main lobby, a large three-floor affair with balconies from the other floors – although, the glass elevator shaft ran through the middle of the room, the metal and Perspex elevator itself clearly visible in the middle. As such, a person had to be on the bottom floor to enter the mainframe, there were no other access points to the elevator. Snake could see that the panels on the elevator were lit up.

_Still working, this building must have its own backup generator. Now to get through the guards._

Snake checked his belt.

_One last clip on the G36, damn, that's nowhere near enough. But I do have some grenades from the ammo dump and my pistol. That will have to do._

Snake pulled out two fragmentation grenades from one of his pouches, the round weights comfortable in his hands as he replaced them. Checking the corner again, he saw that the soldiers were still watching the corridors into the room but were beginning to split up from the group they were standing in. One, armed with an M60 light machine gun, was coming his way.

_I have to get him around the corner, and take him out._

As the guard approached, the other soldiers were moving in other directions, so hopefully if he pulled it off, no-one would notice Snake removing one of their number. The guard's heavy, clumping footsteps approached Snake's position.

Snake, taking a quiet breath, pressed his fist against the wall, and knocked softly. Snake operated by ear: the guard's footsteps abruptly stopped, and the rustling of him readying his weapon were clear. Snake waited, and waited. Agonising seconds crept by slow as minutes, the guard's quiet steps drawing closer.

_Now!_

Snake darted around the corner, the man's surprise visibly in his eyes as a shadow-covered man leapt out of the darkness and grabbed the man's neck. Dragging him around the corner, Snake pressed in the right places, and twisted, hard. The crunching pop of the man's neck snapping was muted by the corridor and walls, as well as Snake's precision.

Dropping the body, Snake waited, taking the man's machine gun and turning off the light, dropping his own rifle carefully.

_This should do the trick. I don't think anyone heard me._

Checking the chamber and feed of bullets from the machine gun, Snake crept around the corner in a crouch, keeping low. Coming up behind a small crate, he got out his two grenades. Now fully in cover and out of sight, Snake pulled the pins on them one at a time and threw them into the room, at the thickest groups of soldiers, in all about seven men. The men's cries of alarm as the grenades clacked against the floor were drowned out a moment later by the loud explosions as they detonated. Snake was already moving into the room, firing the M60 in short bursts at each remaining soldier as they sporadically fired in many directions, some squeezing the triggers of their guns as they died. The sudden burst of gunfire and activity was over almost as quickly as it began. Snake stood breathing quickly, his gun barrel smoking and bodies sprawled across the room. Walking to the elevator, he threw his gun to the ground and drew his pistol.

When he was inside, he pressed the up button and the lift doors closed smoothly before it began to rise quickly. When it reached the top, Snake readied his gun and walked slowly through the doors out into the mainframe entrance room. The only feature here was a large metal door, with a keypad on the side – upon closer examination; Snake noticed that the keypad was already unlocked.

_They're in there._

Snake pushed the door open and walked into the mainframe room. Servers lined either side of the walkway to the centre in neat rows, whirring away quietly. It was cold in the room, Snake noticed. His breath frosted in front of his face, and his fingertips were getting cold. Snake crept silently towards the centre, but before he was halfway there, clumping footsteps approached and a man stepped into view: an old man, with greying hair and a beard, carrying a sword in one hand and a submachine gun in the other.

"Big Boss? It can't be!" Snake said loudly, despite his shock he trained his gun on the man's chest.

"I am not Big Boss, brother." The man said, gesturing to his eyes with a hint of amusement in his voice. Snake halted.

_Two eyes? Brother? Just who the hell is this guy?_

"Who are you?" Snake demanded, his anger and confusion slipping into his gravelly tones.

"You know me, Snake. Or should I say, David?" The man said, keeping his cold blue eyes fixed on Snake's grey ones. "I am your brother, Snake."

"I killed my brother!" Said Snake, remembering Liquid, who was at least the same age as him, this man looked more like Big Boss than anyone else.

"Did you think there was only one?" The man guffawed, his harsh laughter ringing out across the room. "No Snake, there were three of us. I am the third, and greatest of all. I am Solidus Snake."

"Solidus, huh? Why aren't you the same age as me then?" Snake asked.

"Accelerated ageing," Solidus remarked with disgust, "Whereas you and Liquid were created to live as soldiers, I was created to exist for a finite period of time. I will die before I reach half a normal human lifespan. And whereas you and Liquid split the old man's genes between you, I am a _perfect_ clone of Big Boss." Snake thought he heard a hint of pride in Solidus' tone.

"You have seen me before, you know. Not as Solidus, but as George Sears," Solidus said.

"The ex-president? You were in office during Shadow Moses!" Snake realised. "And you were supposed to have died in the Paris hotel bombing less than four months ago! A crime you blamed on me!" Snake was yelling now, seething with rage.

"Ha! I had hoped you would like that little stunt. But if you were wondering why," Solidus replied, "I had to die to escape _their_ retribution. _They_ couldn't know that I had planned to steal REX from Shadow Moses, to fight back at them and end their reign." Solidus explained.

"Who are they? Who the hell are talking about!?" Snake roared, raising his gun back to aim at Solidus' face.

"Why, Snake, you mean to tell me you didn't know?" Solidus asked sarcastically. "A group of people, an organisation bent on controlling the world. A group known only as the _Patriots_." Solidus spat the name out venomously. "We aren't free, Snake. No-one is. Me, you, Liquid, we were all created by this group, we were all exploited by them and their control is extending to cover the entire planet."

"So why do you need the Metal Gear data?" Snake asked quietly.

"We need it to find the Gear. When I do, well, you'll see." Solidus smiled coldly at that.

"Enough! Where's Orson?" Snake shouted.

Solidus turned over his shoulder and called out. "Bring him through, Colonel!"

A man pulled Orson into view from behind one of the servers, a man with green eyes and a side of his face severely burned. Snake pointed his gun at him. With adrenaline pumping through his veins he looked Orson in the eye.

_**To be **_**_concluded..._**


	14. Chapter 12: Showdown

**DISCLAIMER**

**Firstly, I apologise deeply for my extended absence, I was suddenly bogged down with work, coursework and trouble with no visible conclusion. I tried to finish the story but never found enough time to just sit down and do it. So I am sorry, readers. Now, I am happy and a little sad to say this is the second last chapter in my fic, though the last chapter will simply be a nice epilogue, to tie it all together (expect that soon). It has been an interesting experience writing for the website and unleashing my creativity properly for the first time. Thank you for all the views, reviews and support for my first, clunky endeavour into the world of FanFiction. I have a few ideas in the pipeline, so I don't think this is the last you will see of me yet! In the mean time, read on!**

**MrStagg**

No!

Before anyone could react, a shot rang out, and Orson's body hit the floor, an exit wound in the side of his head from where the Colonel's bullet had punched through it. For a moment, no-one moved, as Snake yelled in anger.

"He was a civilian!" Snake's hands shook as he rapidly swapped aim between Solidus and his henchman.

Solidus laughed mirthlessly. "A waste, I know. But you'll be glad to know he didn't give you up when we interrogated him." Snake growled, his anger giving him strength. "Ah, Snake, you should have joined us when you had the chance, imagine the work we could have done together! Instead, you have only proven to disappoint me." Solidus' voice turned cold and hateful.

Snake, switching his aim to the Colonel, looked at Solidus. "You know, I think it's time you shut up and dropped dead. You say you are the true descendent of Big Boss? I guess you didn't know I burned him alive." Snake taunted darkly, noticing a sudden widening of Solidus' eyes. "And now that you killed an innocent man, I have to put you down, too."

Solidus simply turned to the Colonel, who had his MP5 pointed at Snake, and said "take him."

Snake fired three bullets in rapid succession, as he sprinted to the right, into the rows of computer servers, as the Colonel's burst of gunfire hit the walls and some of the other electrical equipment and destroying it, throwing sparks and shards of circuit boards outwards for several metres. As quickly as the two men had opened fire on each other, the room was silent, save for Solidus' clumping footsteps as he sprinted from the room.

_Shit, I can't let Solidus get away! They have the data!_

Just as Snake began to creep between the server towers, he heard a voice from across the room.

"Ha ha, I am going to enjoy killing you, Snake." The Colonel called out. "I'm surprised you don't remember me. We've met before, back at Shadow Moses. I was one of the Genome Soldiers stationed on the base. When you killed Liquid, you took away my shot at fixing my faulty genes, Snake. Then when the main hangar blew I lost half of my face to the explosion. Even if killing you won't save my life, it will give me revenge." Snake could hear his footsteps from across the room.

Snake had been moving slowly around the edges of the servers throughout the Colonel's speech, and he was beginning to close on him. He stopped a moment, though, and holstered his gun.

_He wants to make this personal._

Snake spoke to the room. "If you think you can take me, let's settle this like men." And Snake walked out onto the central platform, where there was only a small computer desk, mounted on a large octagonal platform with stairs on four sides. And sure enough, the Colonel stepped out from behind a server, and threw his gun to the floor as he walked up towards Snake.

"Time for you to die." Snake growled menacingly.

Stepping forwards, his hands raised in a guard, as the Colonel and he began to circle each other, gauging their stances and positions. The Colonel's eyes tightened a moment before his fist came flying from the right, Snake reacting with an elbow block and a sharp jab to the Colonel's jaw, which he dodged and stepped back, returning to circling Snake. Snake threw a low punch at the Colonel's chest, then another at his head, then a knee kick to the groin, which he only barely managed to block. Snarling, the Colonel launched himself at Snake, his fists a blur as he rained attacks onto Snake's arms and upper body.

_Gotcha._

Snake slammed his head into the Colonel's who reeled in pain and disorientation, and before he could recover Snake pressed the advantage, hammering continual blows on him, and despite the Colonel's desperate defence, Snake felt a few ribs, his nose and his collarbone break, and did not stop. Snake's mind became a blur, the Colonel's and Liquid's faces merging into one and before he knew it, he roared in hatred and threw his fist with all his might into the Colonel's face, hearing his neck snap. The sound echoed across the room as in the last moments of his rage, Snake drew his knife from its sheath and rammed it into the Colonel's chest.

Panting with exertion, Snake looked down at the crushed, bleeding mess that used to be the Colonel.

_Damn, I lost control. Now I have to get back on track!_

Wrenching his knife free, Snake turned to the computer console, and plugged in the USB drive Otacon had given him, and by the time he had leaned over the keyboard the program pre-loaded on it had begun attacking and overwhelming the security measures ArmsTech had put in place. Pressing his CODEC, Snake concentrated on his task.

"Otacon, I am inside the network, where do I need to go?"

_"Snake, it's good to hear you're alright! Oh, the data! Now, I need you to find the computer's local disk drive and find any folders that might be related to DARPA, Metal Gear or Shadow Moses. Copy them onto the drive."_

"Got it Otacon. I am transferring the files now."

Snake caught a glimpse of something as some image files copied over.

_Hm, RAY? What the hell were ArmsTech working on?_

Before Snake could investigate, the flash drive bleeped and the copying was done. Practically tearing it out of the computer, Snake sprinted back to the elevator, and when it completed its descent, was already running back to the lobby.

"Otacon?"

_"What is it, Snake?"_

"Are you tracking the helicopters hovering over the base?"

_"Of course. They seem to be pulling back. I will be inbound by helicopter shortly."_

_Shit._

"Otacon, they're pulling out completely and I have to pursue! I will explain why later!"

Snake was running as fast as he had ever run, his boots clumping on the marble floors, past bullet holes, bodies and shell casings. He made his way back to the lobby and jumped through the doors, in time to see the helicopters lifting high enough to fly away, in the direction of the rising sun to the east.

_They're going to get away!_

Snake turned, panting for breath, and something caught his eye: A black dirt bike, with the keys in the ignition. Running over, he climbed on and turned the keys, the engine roaring to life. He engaged the clutch and the throttle, the bike hurtling off along the dirt roads, in fast pursuit of the helicopters.

**Inside Solidus' helicopter...**

Solidus looked out of the window at the last remaining helicopter of the forces he originally deployed. The smoking ruins of the base were passing in a blur below them. But despite the mission's success Solidus could not shake the sudden doubts that entered his mind.

_I have the data. Snake is an irrelevance, nothing more. But still... one man managed to cause this much destruction? He answers to no-one but himself, and now he has a vendetta._

Solidus sighed tiredly to himself, letting fatigue catch up to him slowly, when suddenly he heard something faint on the wind. Marching past the remaining Sons of Liberty soldiers in the helicopter, he ordered the rear hatch to open. As it opened, the base sprawling out before him, he saw something moving at speed along the roads.

_It can't be..._

**On the ground...**

Snake was driving full pelt after the helicopters, and now he had some firepower. Two free-fire rocket launchers that he managed to snag from a storehouse on the road when he stopped a moment, easily powerful enough to take out both of the remaining helicopters. Mounting one on his shoulder, Snake sped up, using only one hand to drive and gunning the acceleration.

"Turn us about!" Solidus roared to the pilots, as Snake approached on his motorcycle, the helicopters sweeping around wide arcs in unison. Now, out in the open desert, with the sun lighting their battlefield, Snake sped towards them, his launcher raised.

Snake maintained a steady aim on the flanking helicopter, aiming to take them out first and then focus on Solidus. Within in a few seconds, still travelling at speed, the target helicopter entered range.

_Firing one of these one-handed will be difficult. Come on..._

Snake aimed, and took a deep breath. As the sound of the Bike's engine and the increasingly loud rotors of the helicopters were drowned by an oppressive silence, Snake thumbed the trigger.

_Now._

Snake pressed the trigger firmly. What followed was a whooshing noise, combined with intense heat in front and behind him, before the helicopter exploded in a fireball, pieces of fuselage and shrapnel flying outwards as its fuel caught fire, the flaming carcass plummeting towards the ground where Snake was driving. Throwing away the first launcher, Snake sped around to the side as the helicopter's wreckage smashed into the sand and slid several meters straight towards where he last stood. Readying the second launcher, Snake took aim at Solidus.

"Take him out!" Solidus roared to his pilot, who nodded, activating the missile pods on either side of the helicopter before focusing aim on Snake.

Snake roared a yell of defiance as he fired the second missile, just as the helicopter opened fire.

It all happened slowly. Snake was on the bike one moment, then was being thrown through the air to the side, spinning at the next. He did not remember hitting the ground, but he could see the fireball expanding from where he was a few seconds ago as seemingly minutes ticked by, flying and twisting, no thoughts in his mind as he smashed into the sand.

Snake blacked out...


	15. Epilogue: How About New York?

**DISCLAIMER**

**I know I said most of my "thank you" bits in the previous chapter, but I will make my conclusion here. I thank everyone who read, reviewed, favourited and followed this story, it has been quite the journey, my first foray into proper creative writing and I am impressed beyond words at the positive support and response this got, so in short, thank you everyone here at FanFiction. Now, I present the Epilogue of my story.**

**MrStagg**

**Three weeks later...**

The New Year's Day of 2007 had been and gone when Snake had woken up. Otacon had found him half-buried in the desert, covered in cuts, bruises, with fractured bones and serious burns across his body. Around him lay the wreckage of one of Solidus' helicopters, combined with the scorched remains of Snake's borrowed motorbike. Otacon had loaded him onto his helicopter, a small civilian model, and flown him back to Boston after stabilising him. Following this, Snake had lain unconscious in a makeshift hospital, while Otacon had helped fix the damage, yet he feared the wounds Snake had sustained, at his age, would cause permanent damage to his physique. Even with Snake's advanced genetics, injuries of such a serious nature could mean that he would never again operate as he used to.

Snake opened his eyes, looking above at the concrete ceiling of the Boston HQ.

_Ow, my head..._

Snake pushed himself up slightly, wincing at the sudden flare of pain that shot up one side of his arm. At the foot of the bed, mounted on the wall was a large mirror, and Snake's eyes widened at what he saw.

His face was more hollowed than he had seen it in recent years, the cheeks visibly more gaunt than they used to be, and the majority of his upper body and shoulders were covered in large gashes, cuts, bruises and abrasions. Bandages were strewn sporadically across his person, and Snake sat, simply staring into the mirror for the next few minutes, trying to remember how he had ended up back in Boston.

_Fire... missiles? Yes, the helicopters... I must have been badly injured, probably knocked out. Thank God Otacon found me._

Snake slowly pulled back the covers, and turned so his legs hung off the bed. However, this effort already had him gasping as nearly every part of his body sent twinges and stabs of pain all over. Waiting for a minute, Snake calmed his breath, returning to the serene thoughts of his old house in Alaska...

Yet this time, Snake felt unease even here, in a place where he could calm himself. On the horizon, across the snow, he saw a man. A tall, old man with white hair and a sword...

Snake snapped back to reality.

_Come on, pull it together. Get up and find Otacon._

Snake placed his arm against the bedspread, and carefully put weight on his bare feet, his legs shaking already. But slowly enough Snake was once again standing, his statue imposing even in its current state. Now, with care and one hand against the wall, Snake put one foot in front of the other, and cautiously shuffled to the stairs, where he grasped the handrail tightly, climbing down to the main area of the basement.

Otacon turned in his chair and pushed up his glasses.

"Snake, you're up!" He said cheerfully, moving over to him and helping him into a chair, before returning to his computer.

"What happened? My memory is so hazy." Snake asked, his voice currently sounding even raspier than usual, most likely due to thirst.

"I found you next to one of Solidus' helicopters, badly injured. I took you to a secure location and stabilised you before I flew you here and patched you up as best I could. That was three weeks ago. Listen Snake," Otacon said, his tone suddenly becoming serious, "you have been very badly hurt. I tried to fix what I can, but..."

"But what?"

"I don't think by my predictions that you will ever reach the same level of fitness you were before. You're getting too old to just get back up again." Otacon looked Snake in the eye.

"Hmm..." Snake turned, looking nowhere in particular and started to think.

_This means I am going to have to adapt my technique. I need to take less punishment in battle. This will take some training._

"Have you found Solidus or anything about him or the Sons of Liberty?" Snake asked quickly, changing the subject.

"No, he's dropped back off the radar. Before he became President George Sears, I can't find anything on him... strange that he can hide himself so well." Otacon tapped away at his computer, effectively ending the conversation.

**A few days later...**

Snake's arm wrapped around the training mannequin, as he placed the combat knife to its throat and pulled across, the serrated edge scraping against the wood.

_Dead, completely silent. This new technique is working._

Snake had taken to basic fitness re-training, combined with workouts suited for people aged between forty and sixty, such as yoga and cardio work. Even though his body screamed out in pain, Snake trudged on, and his fitness was beginning to improve. He was working on adapting his CQC, adding in more knife-work to minimise his own injuries, and with more emphasis on holds, locks, flips and grapples to prevent extended martial arts standoffs.

_I almost fight like an old man now, ha ha._

Just then, Otacon's voice called up from the basement centre, seriousness could be heard in his tone.

"Snake, how would you feel about New York?"

_New York?_

_Why not?_

-THE END-


End file.
